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I have a LVM volume set up with several harddrives, and one of them seems to be failing, or at least something strange is going on. Every time the logical volume series sees heavy write activity, the running program (rTorrent most of the time) crashes, and dmesg reports

ata6.00: exception Emask 0x10 SAct 0x0 SErr 0x1810000 action 0xe frozen
ata6.00: irq_stat 0x00400000, PHY RDY changed
ata6: SError: { PHYRdyChg LinkSeq TrStaTrns }
ata6.00: failed command: FLUSH CACHE EXT
ata6.00: cmd ea/00:00:00:00:00/00:00:00:00:00/a0 tag 0
         res 40/00:2c:ff:e3:e3/00:00:39:00:00/40 Emask 0x10 (ATA bus error)
ata6.00: status: { DRDY }
ata6: hard resetting link
ata6: SATA link up 3.0 Gbps (SStatus 123 SControl 300)
ata6.00: configured for UDMA/133
end_request: I/O error, dev sdf, sector 0
ata6: EH complete
I/O error in filesystem ("dm-3") meta-data dev dm-3 block 0x640092a       ("xlog_iodone") error 5 buf count 32768
xfs_force_shutdown(dm-3,0x2) called from line 1043 of file fs/xfs/xfs_log.c.  Return address = 0xffffffff8119b919
Filesystem "dm-3": Log I/O Error Detected.  Shutting down filesystem: dm-3
Please umount the filesystem, and rectify the problem(s)
xfs_force_shutdown(dm-3,0x2) called from line 811 of file fs/xfs/xfs_log.c.  Return address = 0xffffffff8119ccfb
Filesystem "dm-3": xfs_log_force: error 5 returned.
Filesystem "dm-3": xfs_log_force: error 5 returned.
Filesystem "dm-3": xfs_log_force: error 5 returned.
Filesystem "dm-3": xfs_log_force: error 5 returned.
Filesystem "dm-3": xfs_log_force: error 5 returned.
Filesystem "dm-3": xfs_log_force: error 5 returned.
... and so on

The volume itself:

--- Logical volume ---
  LV Name                /dev/storage/series
  VG Name                storage
  LV UUID                sF6I3A-Ttt5-PEml-BY5i-edOV-43ha-5P75Z3
  LV Write Access        read/write
  LV Status              available
  # open                 1
  LV Size                2.86 TiB
  Current LE             748800
  Segments               29
  Allocation             inherit
  Read ahead sectors     auto
  - currently set to     256
  Block device           253:3

I then umount all the LVM-volumes, and tries to run xfs_check on one (all the logical volumes are using XFS). It says

ERROR: The filesystem has valuable metadata changes in a log which needs to be replayed. Mount the filesystem to replay the log, and unmount it before re-running xfs_check. If you are unable to mount the filesystem, then use the xfs_repair -L option to destroy the log and attempt a repair. Note that destroying the log may cause corruption -- please attempt a mount of the filesystem before doing this.

so I go ahead and mount it, which works fine, then unmount again so I can run the check. This runs for a while, until it is killed for using too much memory.

# xfs_check /dev/storage/series 
/usr/sbin/xfs_check: line 31: 14350 Killed 
                xfs_db$DBOPTS -F -i -p xfs_check -c "check$OPTS" $1

dmesg then reports

xfs_db invoked oom-killer: gfp_mask=0x280da, order=0, oom_adj=0
xfs_db cpuset=/ mems_allowed=0
Pid: 14350, comm: xfs_db Tainted: P           2.6.32-gentoo-r7 #1
Call Trace:
 [<ffffffff81067aec>] ? 0xffffffff81067aec
 [<ffffffff8107a848>] 0xffffffff8107a848
 [<ffffffff8104ee2c>] ? 0xffffffff8104ee2c
 [<ffffffff8107ac83>] 0xffffffff8107ac83
 [<ffffffff8107adf1>] 0xffffffff8107adf1
 [<ffffffff8107d460>] 0xffffffff8107d460
 [<ffffffff8129d69e>] ? 0xffffffff8129d69e
 [<ffffffff8108a40d>] 0xffffffff8108a40d
 [<ffffffff8108bd67>] 0xffffffff8108bd67
 [<ffffffff810258ff>] 0xffffffff810258ff
 [<ffffffff8140290f>] 0xffffffff8140290f
Mem-Info:
DMA per-cpu:
CPU    0: hi:    0, btch:   1 usd:   0
CPU    1: hi:    0, btch:   1 usd:   0
DMA32 per-cpu:
CPU    0: hi:  186, btch:  31 usd: 103
CPU    1: hi:  186, btch:  31 usd: 177
Normal per-cpu:
CPU    0: hi:  186, btch:  31 usd:  35
CPU    1: hi:  186, btch:  31 usd: 155
active_anon:717606 inactive_anon:271926 isolated_anon:0
 active_file:155 inactive_file:217 isolated_file:0
 unevictable:0 dirty:0 writeback:48 unstable:0
 free:6959 slab_reclaimable:1102 slab_unreclaimable:4133
 mapped:156 shmem:0 pagetables:3644 bounce:0
DMA free:15888kB min:28kB low:32kB high:40kB active_anon:0kB inactive_anon:0kB active_file:0kB inactive_file:0kB unevictable:0kB isolated(anon):0kB isolated(file):0kB present:15272kB mlocked:0kB dirty:0kB writeback:0kB mapped:0kB shmem:0kB slab_reclaimable:0kB slab_unreclaimable:0kB kernel_stack:0kB pagetables:0kB unstable:0kB bounce:0kB writeback_tmp:0kB pages_scanned:0 all_unreclaimable? yes
lowmem_reserve[]: 0 2999 4009 4009
DMA32 free:10020kB min:6052kB low:7564kB high:9076kB active_anon:2377112kB inactive_anon:594248kB active_file:252kB inactive_file:268kB unevictable:0kB isolated(anon):0kB isolated(file):0kB present:3071904kB mlocked:0kB dirty:0kB writeback:16kB mapped:196kB shmem:0kB slab_reclaimable:1620kB slab_unreclaimable:3980kB kernel_stack:56kB pagetables:3636kB unstable:0kB bounce:0kB writeback_tmp:0kB pages_scanned:800 all_unreclaimable? yes
lowmem_reserve[]: 0 0 1010 1010
Normal free:1928kB min:2036kB low:2544kB high:3052kB active_anon:493312kB inactive_anon:493456kB active_file:368kB inactive_file:600kB unevictable:0kB isolated(anon):0kB isolated(file):0kB present:1034240kB mlocked:0kB dirty:0kB writeback:176kB mapped:428kB shmem:0kB slab_reclaimable:2788kB slab_unreclaimable:12552kB kernel_stack:1008kB pagetables:10940kB unstable:0kB bounce:0kB writeback_tmp:0kB pages_scanned:2872 all_unreclaimable? yes
lowmem_reserve[]: 0 0 0 0
DMA: 0*4kB 0*8kB 3*16kB 3*32kB 2*64kB 0*128kB 1*256kB 0*512kB 1*1024kB 1*2048kB 3*4096kB = 15888kB
DMA32: 459*4kB 1*8kB 1*16kB 1*32kB 1*64kB 1*128kB 1*256kB 1*512kB 1*1024kB 1*2048kB 1*4096kB = 10020kB
Normal: 482*4kB 0*8kB 0*16kB 0*32kB 0*64kB 0*128kB 0*256kB 0*512kB 0*1024kB 0*2048kB 0*4096kB = 1928kB
2990 total pagecache pages
2626 pages in swap cache
Swap cache stats: add 129611, delete 126985, find 334/869
Free swap  = 0kB
Total swap = 498004kB
1048560 pages RAM
34218 pages reserved
1846 pages shared
1006066 pages non-shared
Out of memory: kill process 14350 (xfs_db) score 105765 or a child
Killed process 14350 (xfs_db)

The memory problems are most likely unrelated, though I don't know why xfs_check should need that much.

smartctl has this to say about the drive:

# smartctl -a /dev/sdf
smartctl 5.39.1 2010-01-28 r3054 [x86_64-pc-linux-gnu] (local build)
Copyright (C) 2002-10 by Bruce Allen, http://smartmontools.sourceforge.net

=== START OF INFORMATION SECTION ===
Model Family:     Western Digital Caviar Blue Serial ATA family
Device Model:     WDC WD5000AAKS-00YGA0
Serial Number:    WD-WCAS80682099
Firmware Version: 12.01C02
User Capacity:    500,107,862,016 bytes
Device is:        In smartctl database [for details use: -P show]
ATA Version is:   8
ATA Standard is:  Exact ATA specification draft version not indicated
Local Time is:    Tue May 17 23:17:17 2011 CEST
SMART support is: Available - device has SMART capability.
SMART support is: Enabled

=== START OF READ SMART DATA SECTION ===
SMART overall-health self-assessment test result: PASSED

General SMART Values:
Offline data collection status:  (0x82) Offline data collection activity
                                        was completed without error.
                                        Auto Offline Data Collection: Enabled.
Self-test execution status:      (   0) The previous self-test routine completed
                                        without error or no self-test has ever
                                        been run.
Total time to complete Offline
data collection:                 (13200) seconds.
Offline data collection
capabilities:                    (0x7b) SMART execute Offline immediate.
                                        Auto Offline data collection on/off support.
                                        Suspend Offline collection upon new
                                        command.
                                        Offline surface scan supported.
                                        Self-test supported.
                                        Conveyance Self-test supported.
                                        Selective Self-test supported.
SMART capabilities:            (0x0003) Saves SMART data before entering
                                        power-saving mode.
                                        Supports SMART auto save timer.
Error logging capability:        (0x01) Error logging supported.
                                        General Purpose Logging supported.
Short self-test routine
recommended polling time:        (   2) minutes.
Extended self-test routine
recommended polling time:        ( 154) minutes.
Conveyance self-test routine
recommended polling time:        (   5) minutes.
SCT capabilities:              (0x303f) SCT Status supported.
                                        SCT Feature Control supported.
                                        SCT Data Table supported.

SMART Attributes Data Structure revision number: 16
Vendor Specific SMART Attributes with Thresholds:
ID# ATTRIBUTE_NAME          FLAG     VALUE WORST THRESH TYPE      UPDATED  WHEN_FAILED RAW_VALUE
  1 Raw_Read_Error_Rate     0x000f   200   200   051    Pre-fail  Always       -       0
  3 Spin_Up_Time            0x0003   226   181   021    Pre-fail  Always       -       3675
  4 Start_Stop_Count        0x0032   100   100   000    Old_age   Always       -       33
  5 Reallocated_Sector_Ct   0x0033   200   200   140    Pre-fail  Always       -       0
  7 Seek_Error_Rate         0x000e   200   200   051    Old_age   Always       -       0
  9 Power_On_Hours          0x0032   061   061   000    Old_age   Always       -       28688
 10 Spin_Retry_Count        0x0012   100   253   051    Old_age   Always       -       0
 11 Calibration_Retry_Count 0x0012   100   253   051    Old_age   Always       -       0
 12 Power_Cycle_Count       0x0032   100   100   000    Old_age   Always       -       32
192 Power-Off_Retract_Count 0x0032   200   200   000    Old_age   Always       -       19
193 Load_Cycle_Count        0x0032   200   200   000    Old_age   Always       -       35
194 Temperature_Celsius     0x0022   112   095   000    Old_age   Always       -       38
196 Reallocated_Event_Count 0x0032   200   200   000    Old_age   Always       -       0
197 Current_Pending_Sector  0x0012   200   200   000    Old_age   Always       -       0
198 Offline_Uncorrectable   0x0010   200   200   000    Old_age   Offline      -       0
199 UDMA_CRC_Error_Count    0x003e   200   200   000    Old_age   Always       -       1
200 Multi_Zone_Error_Rate   0x0008   200   200   051    Old_age   Offline      -       0

SMART Error Log Version: 1
No Errors Logged

SMART Self-test log structure revision number 1
Num  Test_Description    Status                  Remaining  LifeTime(hours)  LBA_of_first_error
# 1  Extended offline    Completed without error       00%     28541         -

SMART Selective self-test log data structure revision number 1
 SPAN  MIN_LBA  MAX_LBA  CURRENT_TEST_STATUS
    1        0        0  Not_testing
    2        0        0  Not_testing
    3        0        0  Not_testing
    4        0        0  Not_testing
    5        0        0  Not_testing
Selective self-test flags (0x0):
  After scanning selected spans, do NOT read-scan remainder of disk.
If Selective self-test is pending on power-up, resume after 0 minute delay.

SMART seems to think there's not much wrong, but obviously something is happening. Unfortunately, I'm not sure what I should try now. I'd like to avoid switching cables or replacing the drive until I know for sure it's needed, but any suggestions are welcome.

Update

As suggested by @Zoredache, I ran badblocks on the drive.

# badblocks -s /dev/sdf
Checking for bad blocks (read-only test): done

and from what I could understand, this is supposed to output a list of bad blocks, meaning it didn't find any…

share|improve this question
    
Quick obvious suggestion, if you don't have a backup, it is now time to create one. Don't wait until it really fails. Is your LVM on top of a RAID, or have you just added several physical devices directly to the Volume group? –  Zoredache May 17 '11 at 21:49
    
If you can afford to take the LVM offline, then you could run a read-only badblocks against the drive. –  Zoredache May 17 '11 at 21:49
    
@Zoredache No RAID, just several physical devices. Got a copy of the important things already. Running badblocks now, and will report back –  PerfectlyNormal May 17 '11 at 21:54
    
Can you physically remove the suspect device from its configuration to test on another machine? If so, run a DFT or MHDD check against the drive to look for bad sectors. –  jmreicha May 20 '11 at 16:55

1 Answer 1

up vote 5 down vote accepted
+50

Try turning off NCQ for the problematic drive (reference: this page and this page)

echo 1 > /sys/block/sdX/device/queue_depth

You might also try changing out the SATA cable to the drive, because a weak/borderline electrical connection might also cause those kinds of errors.

As for your memory problem when running xfs_check; you just need more RAM and/or swap space. That's a pretty big filesystem so I'm not surprised that xfs_check needs a lot of memory.

share|improve this answer
    
Tried the NCQ, and it seems to be working so far. Been doing heavy writing for a few minutes without anything happening. Usually it took less than five. I'll let it run for a while longer just to make sure… –  PerfectlyNormal May 21 '11 at 21:07
    
You got any clever way of making it permanent, or should I just add that echo-line to some bootup script? –  PerfectlyNormal May 21 '11 at 21:07
    
I'm not aware of a "standard" way to modify /sys/* automatically from a boot. For a quick fix, I'd just put that echo line into /etc/rc.local (or your distro's equivalent). –  Heath May 23 '11 at 21:03
1  
you can modify /sys/* with sysfsutils package, see lists.debian.org/debian-user/2009/07/msg02209.html –  tictacbum Mar 14 '13 at 10:10

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